[ensembl-dev] Variant Effect Predictor and VCF output

[cj5 at sanger.ac.uk]

Hi,
For the UK10K project we are using the following script, which optionally
adds GERP and Grantham Matric scores

https://github.com/VertebrateResequencing/vr-codebase/blob/develop/scripts/vcf2consequences_vep

regards
Chris Joyce
Wellcome Trust Sanger Institute


> Hi Fedor,
>
> Currently there is no standard way to describe consequences in VCF;
> the main issue to overcome is that our output format provides one line
> per variant/allele/transcript, whereas VCF mandates one line per
> variant. This means we'd have to squeeze an awful lot of information
> into the INFO column of the VCF.
>
> We should, however, be able to provide at least summary level
> information in the INFO field, and this is what we will look into
> doing, as we have had several requests for VCF output to be a feature
> of the VEP.
>
> I am not aware of any tools to convert, however, I think a simple perl
> script and using the --most_severe or --summary options (both of which
> output only one line per variant) in the VEP you should be able to
> combine the original VCF with the output.
>
> Hope this helps
>
> Will McLaren
> Ensembl Variation
>
> On 9 November 2011 20:03, Fedor Gusev <gusevfe at gmail.com> wrote:
>> Hello everyone.
>>
>> How come it is not possible for VEP to output a vcf file? Are there
>> any tools to convert the output to VCF?
>>
>> --
>> Kind regards,
>> Fedor Gusev.
>>
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>
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